CN109920484A - A kind of analysis method and system of the genetic test data of sequenator - Google Patents
A kind of analysis method and system of the genetic test data of sequenator Download PDFInfo
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Abstract
The invention discloses the analysis methods and system of a kind of genetic test data of sequenator, the analysis method includes: to carry out data Quality Control to the genetic test data in sequenator, the overburden depth for making the coverage rate of amplified fragments reach default coverage rate and amplified fragments reaches default overburden depth and the homogeneity of amplified fragments reaches preset value, filter out invalid amplified fragments data and the invalid base data in pending data, to obtain valid data, the base data with Characteristics of Mutation are filtered out from valid data, base data with Characteristics of Mutation are annotated at many levels, to obtain analysis result data；The analysis system includes quality Control module, analysis module and annotations module.The present invention carries out the Quality Control of batch data data, analysis, annotation to machine data under sequencing on sequenator automatically, substantially reduces and is artificially introduced error, significantly improves the objectivity of genetic test data analysis, and greatly reduces cost.
Description
Technical field
The present invention relates to genetic test data analysis technique fields, specifically for, the present invention be a kind of sequenator use
Genetic test data analysis method and system.
Background technique
Common genetic disease often leads to serious consequence, for example, familial hypercholesterolemia easily leads to individual mistake
Early cardiovascular disease.Nevertheless, Most patients are not made a definite diagnosis yet, even if making a definite diagnosis seemingly certainly, treatment also tend to be
Suboptimum.
Our understandings to this situation are being remolded in the progress of molecular engineering, including improve population prevalence rate.In addition,
In many patients, the polygenes of the range in Disease-causing gene site, the range of the type of rare pathogenic variation and classification and phenotype
Basis exposes potential Pathological Physiology complexity.Certain disease such as familial hypercholesterolemia can be envisioned as one group
Related disease, the presence of clinical symptoms, dyslipidemia, cardiovascular disease family history and rare pvs oryzae and oryzicola, which both increases, examines
Disconnected certainty.Although genetic test is not always helpful or determines, genetic test data can in many cases
Doctor is assisted to carry out reasonable diagnosing and treating.Traditional genetic test data analysing method generally requires to rely on veteran
The accuracy of analysis personnel, analysis are influenced greatly by factors such as analysis personnel's experience, know-how, working conditions, and are needed
The sequencing data of huge data volume is downloaded to be analyzed, thus existing genetic test data analysing method there are objectivity compared with
The problems such as difference, excessive, time cost is excessively high man power and material's investment.
Therefore, the objectivity of genetic test data analysis process how is improved, and genetic test number how is effectively reduced
According to the human cost of analytic process, material resources cost and time cost, becomes those skilled in the art's technology urgently to be resolved and ask
Topic and the emphasis studied always.
Summary of the invention
To solve existing for existing genetic test data analysis scheme, objectivity is difficult to ensure, the time is long, at high cost etc. is asked
Topic, the present invention innovatively provide the analysis method and system of a kind of genetic test data of sequenator, to realize to gene
Data Quality Control, analysis and the annotation of lower machine datamation is sequenced.
To realize the above-mentioned technical purpose, the invention discloses a kind of analysis method of the genetic test data of sequenator,
The analysis method includes the following steps；
Step 1, carry out data Quality Control to the genetic test data in sequenator: the coverage rate for retaining amplified fragments reaches pre-
If the homogeneity that coverage rate and the overburden depth of amplified fragments reach default overburden depth and amplified fragments reaches the base of preset value
Because detection data is as pending data；
Step 2, invalid amplified fragments data and the invalid base data in the pending data are filtered out, thus
To valid data, the base data with Characteristics of Mutation are filtered out from the valid data；
Step 3, the base data with Characteristics of Mutation are annotated at many levels, multi-level annotation procedure is formed
Data and the base data with Characteristics of Mutation collectively as analysis result data.
Further, it in step 2, is determined and is had by way of comparing the valid data and reference sequences data
There are the base data of Characteristics of Mutation, the reference sequences data, which derive from, refers to genome database.
It further, further include that will there are the base data of Characteristics of Mutation to be stored as in the first preset format in step 2
Between file the step of；
In step 3, further include parse first preset format intermediate file and to data obtained after parsing into
The step of row annotates at many levels.
Further, in step 3, the multi-level annotation includes the frequency of mutation annotation in mutational site, mutational site
Genomic locations annotation and the frequency of occurrences annotation in mutational site.
It further, further include the step that analysis result data is stored as to the comment file of the second preset format in step 3
Suddenly.
To realize the above-mentioned technical purpose, the invention also discloses a kind of analysis systems of the genetic test data of sequenator
System, which includes quality Control module, analysis module and annotations module；
The quality Control module, for carrying out data Quality Control to the genetic test data in sequenator: retaining amplified fragments
The overburden depth that coverage rate reaches default coverage rate and amplified fragments reaches default overburden depth and the homogeneity of amplified fragments reaches
To preset value genetic test data as pending data；
The analysis module, for filtering out invalid amplified fragments data and invalid base in the pending data
Data obtain valid data, and for filtering out the base data with Characteristics of Mutation from the valid data；
The annotations module for being annotated at many levels to the base data with Characteristics of Mutation, and is used for
The data and the base data with Characteristics of Mutation that multi-level annotation procedure is formed are collectively as analysis result data.
Further, the analysis module, for by comparing the valid data and reference sequences data
Mode determines the base data with Characteristics of Mutation, and the reference sequences data, which derive from, refers to genome database.
Further, the analysis module, for will have the base data of Characteristics of Mutation to be stored as the first preset format
Intermediate file；
The annotations module, for parsing the intermediate file of first preset format and for obtained after parsing
Data are annotated at many levels.
Further, the multi-level annotation includes the genome position of the frequency of mutation annotation in mutational site, mutational site
Set the frequency of occurrences annotation in annotation and mutational site.
Further, the annotations module, for the analysis result data to be stored as to the annotation of the second preset format
File.
The invention has the benefit that
The present invention can carry out automatically the Quality Control of batch data data, analysis, annotation to machine data under sequencing on sequenator,
Intermediate rarely human intervention is artificially introduced error, significantly improves the visitor of genetic test data analysis to substantially reduce
The property seen, and the duty cycle is shortened, it is suitable for popularization and application.
Detailed description of the invention
Fig. 1 is a kind of flow diagram of the analysis method of the genetic test data of sequenator.
Fig. 2 is a kind of composition schematic diagram of the analysis system of the genetic test data of sequenator.
Specific embodiment
With reference to the accompanying drawings of the specification to a kind of analysis method of the genetic test data of sequenator of the present invention
And system carries out detailed explanation and illustration.
Embodiment one:
As shown in fig. 1, present embodiment discloses a kind of analysis methods of the genetic test data of sequenator, to gene
Lower machine data are sequenced and carry out automatic processing, the present embodiment is that two generation sequencing datas are carried out with automatic, mass analysis, and existing
Technology is compared, and the present invention thoroughly solves the problems such as objectivity existing for traditional artificial analysis method is poor, the time is long, at high cost,
Specifically, which includes the following steps.
Preparation process: experimenter carries out relevant configuration: the present embodiment on server (for example, server was sequenced in two generations)
By taking the genetic test data analysis process of hypercholesterolemia as an example, experimenter completes the base of sequencing in creation sequencing plan
This configuration chooses the related plug-in unit for the analysis of genetic test data (for example, iAnalyses is inserted in plug-in unit analysis option
Part), it is selected from a variety of diseases (for example, hypercholesterolemia, arotic disease, neoplastic hematologic disorder, gynecological tumor etc.) option high
Cholesterolemia option；It carries out number capable of being sequenced to the genetic test of familial hypercholesterolemia after the sequencing is completed in sequenator
Quality Control, analysis and annotation are carried out according to automatic.
Step 1, carry out data Quality Control to the genetic test data in sequenator: the coverage rate for retaining amplified fragments reaches pre-
If the homogeneity that coverage rate and the overburden depth of amplified fragments reach default overburden depth and amplified fragments reaches the base of preset value
Because detection data is as pending data, i.e. the overburden depth of amplified fragments in pending data reach default overburden depth and
The homogeneity of amplified fragments reaches preset value, wherein and preset value can carry out rationally and wise setting as the case may be, this
Embodiment repeats no more.The present embodiment comments this experiment and sequencing by way of carrying out Quality Control to machine data under being sequenced
Estimate, to guarantee the accuracy and reliability of subsequent analysis.
Step 2, invalid amplified fragments data and the invalid base data in pending data are filtered out, to be had
Data are imitated, the base data with Characteristics of Mutation are filtered out from valid data；In the present embodiment step 2, by by significant figure
The base data with Characteristics of Mutation are determined according to the mode compared with reference sequences data, it can be during the comparison process using more
A data analysis parameter compares, so as to improve the accuracy of data analysis, wherein reference sequences data, which derive from, refers to base
Because of a group database.When it is implemented, this step includes that will there are the base data of Characteristics of Mutation to be stored as the first preset format
It can be vcf format that the step of intermediate file, which is the first preset format in the present embodiment,.
Step 3, the intermediate file of the first preset format is parsed first and data obtained after parsing is carried out multi-level
Annotation, specifically the base data with Characteristics of Mutation are annotated at many levels, the data that multi-level annotation procedure is formed with
Base data with Characteristics of Mutation are collectively as analysis result data, to detect all information in mutational site.This step
In rapid, multi-level annotation can annotate the statistical information in mutational site, and multi-level annotation includes the frequency of mutation in mutational site
The frequency of occurrences annotation of annotation, the genomic locations annotation in mutational site and mutational site, in addition, multi-level annotation can also annotate
Upper a variety of diseases, crowd's frequency, protein function prediction, shearing prediction, conservative prediction etc..Finally, this step further includes that will divide
The step of result data is stored as the comment file of the second preset format is analysed, is that the second preset format can be in the present embodiment
Vcf format.
Embodiment two:
As shown in Fig. 2, the present embodiment and embodiment one are based on identical inventive concept, a kind of sequenator use is specifically disclosed
Genetic test data analysis system, it can be understood as genetic test data knowledge solution release system, the present embodiment is by the analysis
System is directly embedded into sequenator, and the process for downloading a large amount of sequencing datas is avoided with this, saves time and storage resource；Specifically
For, which includes: quality Control module, analysis module and annotations module.
Quality Control module, for carrying out data Quality Control to the genetic test data in sequenator: retaining the covering of amplified fragments
The overburden depth that rate reaches default coverage rate and amplified fragments reaches default overburden depth and the homogeneity of amplified fragments reaches pre-
If the genetic test data of value are as pending data.
Analysis module, for filter out invalid amplified fragments data in pending data and invalid base data,
To valid data, and for filtering out the base data with Characteristics of Mutation from valid data.In the present embodiment, mould is analyzed
Block is used for the determining base data with Characteristics of Mutation by way of comparing valid data and reference sequences data,
In, reference sequences data, which derive from, refers to genome database, such as familial hypercholesterolemia knowledge base.In addition, analysis
Module is also used to for the base data with Characteristics of Mutation being stored as the intermediate file of the first preset format；The analysis of the present embodiment
Module can be the genetic test Data Analysis Model of foundation.
Annotations module is initially used for the intermediate file of the first preset format of parsing and for data obtained after parsing
It is annotated at many levels, specifically for being annotated at many levels to the base data with Characteristics of Mutation, and for by multilayer
The data that secondary annotation procedure is formed and the base data with Characteristics of Mutation are collectively as analysis result data.In the present embodiment,
Multi-level annotation includes the frequency of mutation annotation, the genomic locations annotation in mutational site and the appearance in mutational site in mutational site
Frequency annotation.Annotations module is also used to for analysis result data being stored as the comment file of the second preset format.
In the description of this specification, reference term " the present embodiment ", " one embodiment ", " some embodiments ", " show
The description of example ", " specific example " or " some examples " etc. mean specific features described in conjunction with this embodiment or example, structure,
Material or feature are included at least one embodiment or example of the invention.In the present specification, above-mentioned term is shown
The statement of meaning property is necessarily directed to identical embodiment or example.Moreover, specific features, structure, material or the spy of description
Point may be combined in any suitable manner in any one or more of the embodiments or examples.In addition, without conflicting with each other,
Those skilled in the art can be by different embodiments or examples described in this specification and different embodiments or examples
Feature is combined.In addition, term " first ", " second " are used for description purposes only, and it should not be understood as instruction or dark
Show relative importance or implicitly indicates the quantity of indicated technical characteristic.
The foregoing is merely illustrative of the preferred embodiments of the present invention, is not intended to limit the invention, all in essence of the invention
Made any modification, equivalent replacement and simple modifications etc., should all be included in the protection scope of the present invention in content.
Claims (10)
1. a kind of analysis method of the genetic test data of sequenator, it is characterised in that: the analysis method includes the following steps；
Step 1, carry out data Quality Control to the genetic test data in sequenator: the coverage rate for retaining amplified fragments reaches default and covers
The homogeneity that lid rate and the overburden depth of amplified fragments reach default overburden depth and amplified fragments reaches the gene inspection of preset value
Measured data is as pending data；
Step 2, invalid amplified fragments data and the invalid base data in the pending data are filtered out, to be had
Data are imitated, the base data with Characteristics of Mutation are filtered out from the valid data；
Step 3, the base data with Characteristics of Mutation are annotated at many levels, the number that multi-level annotation procedure is formed
According to the base data with Characteristics of Mutation collectively as analysis result data.
2. the analysis method of the genetic test data of sequenator according to claim 1, it is characterised in that:
In step 2, determine that there is Characteristics of Mutation by way of comparing the valid data and reference sequences data
Base data, the reference sequences data, which derive from, refers to genome database.
3. the analysis method of the genetic test data of sequenator according to claim 1 or 2, it is characterised in that:
In step 2, further include the steps that the intermediate file that the base data with Characteristics of Mutation are stored as to the first preset format；
It further include parsing the intermediate file of first preset format and data obtained after parsing being carried out more in step 3
The step of level annotates.
4. the analysis method of the genetic test data of sequenator according to claim 3, it is characterised in that:
In step 3, the multi-level annotation includes the genomic locations annotation of the frequency of mutation annotation in mutational site, mutational site
And the frequency of occurrences annotation in mutational site.
5. the analysis method of the genetic test data of sequenator according to claim 4, it is characterised in that:
In step 3, further include the steps that the comment file that analysis result data is stored as to the second preset format.
6. a kind of analysis system of the genetic test data of sequenator, it is characterised in that: the analysis system include quality Control module,
Analysis module and annotations module；
The quality Control module, for carrying out data Quality Control to the genetic test data in sequenator: retaining the covering of amplified fragments
The overburden depth that rate reaches default coverage rate and amplified fragments reaches default overburden depth and the homogeneity of amplified fragments reaches pre-
If the genetic test data of value are as pending data；
The analysis module, for filtering out invalid amplified fragments data and invalid base number in the pending data
According to, obtain valid data, and for filtering out the base data with Characteristics of Mutation from the valid data；
The annotations module, for being annotated at many levels to the base data with Characteristics of Mutation, and for will be more
The data and the base data with Characteristics of Mutation that level annotation procedure is formed are collectively as analysis result data.
7. the analysis system of the genetic test data of sequenator according to claim 6, it is characterised in that:
The analysis module is dashed forward for determining to have by way of comparing the valid data and reference sequences data
Become the base data of feature, the reference sequences data, which derive from, refers to genome database.
8. the analysis system of the genetic test data of sequenator according to claim 6 or 7, it is characterised in that:
The analysis module, for the base data with Characteristics of Mutation to be stored as to the intermediate file of the first preset format；
The annotations module, for parsing the intermediate file of first preset format and for data obtained after parsing
It is annotated at many levels.
9. the analysis system of the genetic test data of sequenator according to claim 8, it is characterised in that: the multilayer
Secondary annotation includes the frequency of mutation annotation, the genomic locations annotation in mutational site and the frequency of occurrences in mutational site in mutational site
Annotation.
10. the analysis system of the genetic test data of sequenator according to claim 9, it is characterised in that:
The annotations module, for the analysis result data to be stored as to the comment file of the second preset format.
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Application publication date: 20190621 |